Tutorial: nf-selection

Introduction

In 1858, scientists Charles Darwin and Alfred Russell Wallace described for the first time and independently, the principle of natural selection [1]. This revolutionary theory, published in the book “On the Origin of Species by Means of Natural Selection”, articulates the idea that beneficial traits — those characteristics that improve an individual’s chances to survive and reproduce — tend to become more frequent in populations over time [2,3]. A few years later, the Darwinian concept of natural selection was combined with the rediscovery of Mendelian laws to define selection as a change in the allele frequencies of a population by a specific selective pressure [4,5]. The redefinition of the concept of selection from a genetic perspective gave way to the possibility of studying and identifying the impact of selection at the most fundamental level, that is, the genome [4].

Over the past few years, the considerable increase in computational power and the development of next-generation sequencing technologies have given way to the opportunity to identify characteristic patterns of selection in the genetic material of various species and organisms [6]. In doing so, researchers have begun to understand not only the evolution of the populations but the geographical distribution of traits and diseases as well [7,8,9]. Although detection of selection signatures increases our understanding of populations, the required use of statistical and bioinformatics methods represents a barrier for scientists unfamiliar with data manipulation. To overcome this problem, several bioinformatics pipelines have been developed to simplify the steps required to move from genotype data to hypothesis regarding signatures of selection. For instance, the web-based tool “Selection Browser 1.0” has the purpose of determining the action of selection in data from the 1000 genomes project by implementing a series of informative statistics 10. Likewise, Murray Cadzow and collaborators created “Selection Tools”, a pipeline to take Variant Call Format (VCF) through several selection analyses [8]. Although these resources allow the simplified treatment of the genotype data, both are based on the same detection methods - Tajima’s D, CLR, Fay and Wu’s H, XPEHH, iHH, iHS, FST, DAF, and XPCLR -, thus leaving the global overview incomplete.

The Population Branch Statistic (PBS) is a population differentiation-based method with strong power to detect recent natural selection [11]. The Integrated Haplotype Score (iHS) is a linkage disequilibrium-based method to detect recent positive selection. Both statistics have been used together for detecting regions of the genome under selection in several investigations [See references 12-15]. Despite this, there are currently no public bioinformatics tools that allow PBS and iHS to be calculated in an automated way. Here we provide a brief overview and tutorial for nf-selection, a simple Nextflow pipeline for identifying recent signatures of selection in whole-genome genotype data with PBS and iHS. This pipeline compute PBS for any diploid species where genome-wide data is available in a VCF file.

Methods for detecting signatures of selection

The methods for the study of selection can be divided according to the temporal depth over which the selection occurred, the type of selection being investigated, and the approach of each of the methods. This last classification includes frequency-based methods, linkage disequilibrium-based methods, and population differentiation-based methods [3].

Population differentiation–based methods have been widely used to identify selection signals on a timescale in the range of 50,000 to 75,000 years from the present [8,16]. The foundation behind these statistics lies in the fact that separate populations experience different selective pressures, and, as a result, the adaptive traits of one population may be dissimilar from the traits of another. Thus, if the selection is acting at a specific locus of a population, but not at the same locus in a different population, we will observe significantly different allele frequencies. Unlike other approaches, population differentiation–based methods have the ability to detect positive, neutral, and negative selection [3].

The Wright’s Fixation Index (FST) is the most widely used population comparison-based statistic for the detection of selection signals [16]. This metric is responsible for comparing the variation of allele frequencies within and between populations. If there is a marked differentiation at one locus between two populations, FST values will be relatively high. By contrast, if two populations are homogeneous at one locus, the FST values will be relatively small [3]. Over the last few years, a series of statistics have been derived from the FST, among them, we can find the Lewontin-Krakauer Test (LKT), the Locus-specific Length Branch Metric (LSBL), the Cross-Population Composite Likelihood Ratio (XP-CLR), and the Population Branch Statistic (PBS) [3].

Linkage disequilibrium-based methods detect selection signals by searching for regions with long haplotypes. This type of statistics are particularly useful for detecting variants that have undergone partial or incomplete selective sweeps (variants that have not been fixed in the population). A large percentage of LD-based tests derive from the Extended Haplotype Homozygosity Statistic (EHH). The EHH test application defines a core region (eg, an allele with hypothesis of selection) and specifies an upstream and downstream distance from the variant. Then, calculates the probability of obtaining an identical core region by randomly taking two chromosomes [3].

Starting from the EHH statistic, Voight et al. developed the Integrated Haplotype Score (iHS) analysis in 2006, which compares the area under the curve defined by the EHH test [17]. Another variation of the EHH is the Cross Population Extended Haplotype Homozygosity (XP-EHH) statistic [18], which compares the length of haplotypes between populations. Other statistics based on linkage disequilibrium include the long-range haplotype (LRH)[19], LD decay (LDD)[20], and identity-by-descent (IBD) tests [21,22]. The focus of this work will be entirely directed at PBS and iHS.

Description of Population Branch Statistic (PBS)

Although the FST can be used to detect potential targets of natural selection, a simple ranking of FST values cannot reveal which of the two populations was affected by selection [11]. To overcome this issue, Yi and collaborators described for the first time the PBS.

This statistic includes two related populations - pop1 and pop2 - and a third, more distantly related population - popout -. Then, by comparing the three pairwise FST values between these three samples - pop1vspop2, pop1vspopout, and pop2vspopout - it can estimate the frequency change that occurred in the population of interest (pop1) since its divergence from its related population (pop2). Therefore, a population’s PBS value represents the amount of allele frequency change at a given locus since its divergence from the other two populations [11].

This approach is pretty similar to the LSBL metric, in which the FST is pair-wise calculated from three or more populations to identify population-specific changes in allele frequency given a genetic and demographic context [3]. Even though LSBL and PBS share the same basis, the last one uses the classical log transformation by Cavalli-Sforza [11,17].

Description of integrated Haplotype Score (iHS)

The integrated Haplotype Score (iHS) statistic is based on the Extended Haplotype Homozygosity (EHH) test first proposed in 2002 by Sabeti et al [5]. The EHH test estimates the probability that two randomly selected chromosomes are homozygous for all the variants found in a genetic distance X. The value of EHH is computed on a scale from 0 (no homozygosity, all haplotypes are different) to 1 (complete homozygosity, all haplotypes are the same). When an allele under selection increases its frequency, high levels of haplotypic homozygosity are observed. Therefore, in EHH versus Distance plots the area under the EHH curve will usually be larger for an allele under selection compared to that observed for a neutral allele.

Voight et al captured the previously described effect by calculating the integral of the observed decrease in homozygosity from a specific core region until reaching an EHH value equal to 0.05. This integrated EHH (iHH) value is denoted as iHHA if it is computed with respect to the ancestral allele and as iHHD if it is computed with respect to the derived allele. Thus, the iHS is obtained as follow: In(iHHA/iHHD).

Bioinformatics workflow: nf-selection

To automate the process of selection signatures detection with PBS and iHS, we developed nf-selection, a bioinformatics Nextflow pipeline that achieves the implementation of the analyses required to obtain results. The pipeline, and scripts developed for operation are publicly available via GitHub.

Pipeline operation

nf-selection runs within a standard Linux distribution (successfully tested in Ubuntu 18.04 LTS and Ubuntu 20.04 LTS) and requires the installation of publicly available software. The main input of the tool is a VCF file storing the genotype data of interest. VCF files are tab-delimited texts containing information about chromosomes, coordinates, reference, and alternative alleles, as well as genotypes per ID sample [19]. Each calculation of nf-selection is realized in a high-level parallel computational environment, allowing the execution of many jobs across many compute nodes.

Investigating Selection at the Human Lactase Gene Locus as an Example

To better understand the usage of nf-selection, we are presenting a step-by-step tutorial on how to run the pipeline. To do so, we are employing genotype data from chromosome 2 of the human genome, derived from data downloaded from the 1000 Genomes Project. Of interest is the region around the gene encoding lactase (LCT - hg38 chr2:135,787,850-135,837,184), which has shown evidence of selection over the past 5000–10,000 years in African and European populations.

As a first step, we are going to download the VCF file for chromosome 2 (hg38 version) from the 1000 Genomes Browser (http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/). We will create a new directory named “1000G_data” and then use wget to download the VCF file.


mkdir 1000G_data
cd 1000G_data
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr2.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz

Next, we will create three different .txt files with the IDs of individuals that are going to be used for this analysis. Our population of interest is going to be coded as CEU (Europeans), and the ingroup and outgroup populations for PBS will be CHB (Han Chinese) and YRI (Yorubas) respectively. To obtain the IDs for individual belonging to these populations we can access to: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel.


wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel

grep "CEU" integrated_call_samples_v3.20130502.ALL.panel | cut -f1 > ceu_individuals.txt
grep "CHB" integrated_call_samples_v3.20130502.ALL.panel | cut -f1 > chb_individuals.txt
grep "YRI" integrated_call_samples_v3.20130502.ALL.panel | cut -f1 > yri_individuals.txt

## We will create an additional file with all the samples
cat ceu_individuals.txt chb_individuals.txt yri_individuals.txt > all_samples.txt

By using our new created “all_samples.txt” file, we will filter our original VCF to only keep CEU, CHB and YRI individuals. Additionally, we will filter the VCF to only keep nucleotides between 100,000,000 and 150,000,000 range.

vcftools --gzvcf out.vcf.gz --out filtered_vcf --keep all_samples.txt --chr 2 --from-bp 100000000 --to-bp 150000000 --recode

Note: Users must have vcftools installed on the chosen Linux distribution (For documentation see: https://vcftools.sourceforge.net/man_latest.html#SITE%20FILTERING%20OPTIONS)

We will also create a VCF file with only the individuals in our study population (CEU). To do so, we will use “ceu_individuals.txt” to filter our previous VCF (filtered_vcf.recode.vcf).

vcftools --vcf filtered_vcf.recode.vcf --out ceu_filtered --keep ceu_individuals.txt --recode
Running nf-selection

Once our VCF file is filtered, we can proceed with the usage of nf-selection. The first step consist on downloading the pipeline into the Users interface. This step will create a folder named nf-selection with several sub-folders. For convenience, we will move our filtered VCF to the path “test/data/pbs_files/”, the files with population IDs to the path “test/data/pbs_files/”, and the VCF file with only CEU individuals to the path “test/data/ihs_files/”

git clone https://github.com/fernanda-miron/nf-selection.git 
mv 1000G_data/filtered_vcf.recode.vcf nf-selection/test/data/pbs_files
mv 1000G_data/*.txt nf-selection/test/data/pbs_files
mv 1000G_data/ceu_filtered.recode.vcf nf-selection/test/data/ihs_files

Before running the pipeline, the user must ensure that software from Table 1 is installed and executable from any path.

Software Version URL
Nextflow >= 20.0 https://www.nextflow.io/docs/latest/getstarted.html
VCFTools >= 0.1.15 https://vcftools.sourceforge.net/man_latest.html#SITE%20FILTERING%20OPTIONS
SHAPEIT4 4.2 https://odelaneau.github.io/shapeit4/
samtools > 1.12 http://www.htslib.org/download/
bedtools > 1.12 http://www.htslib.org/download/
R > 4.2.3 https://www.r-project.org/
rehh 3.2.2 https://cran.r-project.org/
dplyr 1.1.0 https://cran.r-project.org/
ggplot2 3.4.1 https://cran.r-project.org/
qqman 0.1.8 https://cran.r-project.org/
vroom 1.6.1 https://cran.r-project.org/
tidyr 1.3.0 https://cran.r-project.org/
cowplot 1.1.1 https://cran.r-project.org/
circlize 0.4.15 https://cran.r-project.org/

Once software pre-requirements are satisfied, we need create two different design files (One for PBS and iHS respectively).

Creating a design file for iHS

Since 1000G VCF files are already phased, we will modify the design file (design_file.csv) that is included in the path “nf-selection/test/data/ihs_files”. For cases in which VCF is not phased, see https://github.com/fernanda-miron/nf-selection to find a pre-made design file.

cd nf-selection/test/data/ihs_files
nano design_file.csv

A design file is a csv file that contains information needed to compute iHS. For a phased VCF we need to provide the following information: Number of chromosome, path of the VCF we want to use for iHS computing (ceu_filtered.recode.vcf), path of genetic map for specified chromosome, path of ancestral fasta file for specified chromosome and path for manifest file. Genetic maps and manifest files for hg38 reference can be found at nf-selection/nf_modules/genetic_maps/ and nf-selection/nf_modules/manifest_annotation/ respectively. For our current example, the design file for iHS looks as follow:

chromosome,path_vcf,path_genetic_map,path_ancestral,path_manifest
2,test/data/ihs_files/ceu_filtered.recode.vcf,test/data/ihs_files/chr2.b38.predicted.map,nf_modules/ancestral_fasta/ANCESTOR_for_chromosome_GRCh38_2_1_242193529_1.fa,nf_modules/manifest_annotation/manifest2

After modifying design_file.csv with nano (or text editor of preference), make sure the changes are saved.

Creating a design file for PBS

For PBS design file, we will modify the design file (design_file.csv) that is included in the path “nf-selection/test/data/pbs_files”.

cd nf-selection/test/data/pbs_files
nano design_file.csv

A design file is a csv file that contains information needed to compute PBS. For any VCF file we need to provide the following information: path of the VCF we want to use for PBS computing (filtered_vcf.recode.vcf), path of the file with IDs for our population of interest (ceu_individuals.txt), path of the file with IDs for our ingroup population (chb_individuals.txt) and path of the file with IDs for our outgroup population (yri_individuals.txt). For our current example, the design file for iHS would look as follow:

path_vcf,path_pop1,path_pop2,path_popout
test/data/pbs_files/filtered_vcf.recode.vcf,test/data/pbs_files/ceu_individuals.txt,test/data/pbs_files/chb_individuals.txt,test/data/pbs_files/yri_individuals.txt

After modifying design_file.csv with nano (or text editor of preference), make sure the changes are saved.

Running analysis

Finally, to run the analysis go to “nf-selection2” and run:

bash runtest.sh

If everything worked as expected, you should see the following on your screen

When the analysis is over, your console should look as follows:


Analyzing results.

Once the pipeline has successfully finish all the processes, we can start analyzing our results. Table 2 shows a description of the most important directories and the files that may be useful.

Directory File Description
nf-selection2/test/results/all_chr_ihs final_ihs.tsv A tsv file with iHS absolute values for all SNPs with min_maf=0.05 in VCF
nf-selection2/test/results/all_chr_ihs final_ihs_onepercent.tsv A tsv file with iHS absolute values for the top 1% SNPs with min_maf=0.05 in VC
nf-selection2/test/results/pbs_by_snp pbs.tsv A tsv file with PBS values for all SNPs in VCF
nf-selection2/test/results/pbs_by_snp one_percent_pbs.tsv A tsv file with PBS values the top 1% SNPs in VCF
nf-selection2/test/results/pbs_vs_ihs pbs_vs_ihs.tsv A tsv file with intersection between top 1% values of PBS and iHS
nf-selection2/test/results/annotation annotation.hg38_multianno.txt Annotation of top 1% variants under putative selection

Additionally, we can find several plots for PBS, iHS and the intersection of both plots:

“Manhattan plot for iHS values”
“Histogram distribution for iHS values”
“Manhattan plot for PBS values”
“Histogram distribution for PBS values”
“Circus plot for PBS and iHS”

Finally, by looking at “annotation.hg38_multianno.txt” we can observe SNPs under putative selection in the LCT gene, thus confirming previous hypothesis of selection in European populations and the effectiveness of nf-selection.

Variants under selection in LCT
Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene Xref.refGene cytoBand ExAC_ALL ExAC_AFR ExAC_AMR ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS avsnp147 SIFT_score SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV_pred Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score LRT_pred MutationTaster_score MutationTaster_pred MutationAssessor_score MutationAssessor_pred FATHMM_score FATHMM_pred PROVEAN_score PROVEAN_pred VEST3_score CADD_raw CADD_phred DANN_score fathmm-MKL_coding_score fathmm-MKL_coding_pred MetaSVM_score MetaSVM_pred MetaLR_score MetaLR_pred integrated_fitCons_score integrated_confidence_value GERP++_RS phyloP7way_vertebrate phyloP20way_mammalian phastCons7way_vertebrate phastCons20way_mammalian SiPhy_29way_logOdds Otherinfo1 Otherinfo2 Otherinfo3 Otherinfo4 Otherinfo5 Otherinfo6 Otherinfo7 Otherinfo8 Otherinfo9 Otherinfo10 Otherinfo11 Otherinfo12 Otherinfo13 Otherinfo14 Otherinfo15 Otherinfo16 Otherinfo17 Otherinfo18 Otherinfo19 Otherinfo20 Otherinfo21 Otherinfo22 Otherinfo23 Otherinfo24 Otherinfo25 Otherinfo26 Otherinfo27 Otherinfo28 Otherinfo29 Otherinfo30 Otherinfo31 Otherinfo32 Otherinfo33 Otherinfo34 Otherinfo35 Otherinfo36 Otherinfo37 Otherinfo38 Otherinfo39 Otherinfo40 Otherinfo41 Otherinfo42 Otherinfo43 Otherinfo44 Otherinfo45 Otherinfo46 Otherinfo47 Otherinfo48 Otherinfo49 Otherinfo50 Otherinfo51 Otherinfo52 Otherinfo53 Otherinfo54 Otherinfo55 Otherinfo56 Otherinfo57 Otherinfo58 Otherinfo59 Otherinfo60 Otherinfo61 Otherinfo62 Otherinfo63 Otherinfo64 Otherinfo65 Otherinfo66 Otherinfo67 Otherinfo68 Otherinfo69 Otherinfo70 Otherinfo71 Otherinfo72 Otherinfo73 Otherinfo74 Otherinfo75 Otherinfo76 Otherinfo77 Otherinfo78 Otherinfo79 Otherinfo80 Otherinfo81 Otherinfo82 Otherinfo83 Otherinfo84 Otherinfo85 Otherinfo86 Otherinfo87 Otherinfo88 Otherinfo89 Otherinfo90 Otherinfo91 Otherinfo92 Otherinfo93 Otherinfo94 Otherinfo95 Otherinfo96 Otherinfo97 Otherinfo98 Otherinfo99 Otherinfo100 Otherinfo101 Otherinfo102 Otherinfo103 Otherinfo104 Otherinfo105 Otherinfo106 Otherinfo107 Otherinfo108 Otherinfo109 Otherinfo110 Otherinfo111 Otherinfo112 Otherinfo113 Otherinfo114 Otherinfo115 Otherinfo116 Otherinfo117 Otherinfo118 Otherinfo119 Otherinfo120 Otherinfo121 Otherinfo122 Otherinfo123 Otherinfo124 Otherinfo125 Otherinfo126 Otherinfo127 Otherinfo128 Otherinfo129 Otherinfo130 Otherinfo131 Otherinfo132 Otherinfo133 Otherinfo134 Otherinfo135 Otherinfo136 Otherinfo137 Otherinfo138 Otherinfo139 Otherinfo140 Otherinfo141 Otherinfo142 Otherinfo143 Otherinfo144 Otherinfo145 Otherinfo146 Otherinfo147 Otherinfo148 Otherinfo149 Otherinfo150 Otherinfo151 Otherinfo152 Otherinfo153 Otherinfo154 Otherinfo155 Otherinfo156 Otherinfo157 Otherinfo158 Otherinfo159 Otherinfo160 Otherinfo161 Otherinfo162 Otherinfo163 Otherinfo164 Otherinfo165 Otherinfo166 Otherinfo167 Otherinfo168 Otherinfo169 Otherinfo170 Otherinfo171 Otherinfo172 Otherinfo173 Otherinfo174 Otherinfo175 Otherinfo176 Otherinfo177 Otherinfo178 Otherinfo179 Otherinfo180 Otherinfo181 Otherinfo182 Otherinfo183 Otherinfo184 Otherinfo185 Otherinfo186 Otherinfo187 Otherinfo188 Otherinfo189 Otherinfo190 Otherinfo191 Otherinfo192 Otherinfo193 Otherinfo194 Otherinfo195 Otherinfo196 Otherinfo197 Otherinfo198 Otherinfo199 Otherinfo200 Otherinfo201 Otherinfo202 Otherinfo203 Otherinfo204 Otherinfo205 Otherinfo206 Otherinfo207 Otherinfo208 Otherinfo209 Otherinfo210 Otherinfo211 Otherinfo212 Otherinfo213 Otherinfo214 Otherinfo215 Otherinfo216 Otherinfo217 Otherinfo218 Otherinfo219 Otherinfo220 Otherinfo221 Otherinfo222 Otherinfo223 Otherinfo224 Otherinfo225 Otherinfo226 Otherinfo227 Otherinfo228 Otherinfo229 Otherinfo230 Otherinfo231 Otherinfo232 Otherinfo233 Otherinfo234 Otherinfo235 Otherinfo236 Otherinfo237 Otherinfo238 Otherinfo239 Otherinfo240 Otherinfo241 Otherinfo242 Otherinfo243 Otherinfo244 Otherinfo245 Otherinfo246 Otherinfo247 Otherinfo248 Otherinfo249 Otherinfo250 Otherinfo251 Otherinfo252 Otherinfo253 Otherinfo254 Otherinfo255 Otherinfo256 Otherinfo257 Otherinfo258 Otherinfo259 Otherinfo260 Otherinfo261 Otherinfo262 Otherinfo263 Otherinfo264 Otherinfo265 Otherinfo266 Otherinfo267 Otherinfo268 Otherinfo269 Otherinfo270 Otherinfo271 Otherinfo272 Otherinfo273 Otherinfo274 Otherinfo275 Otherinfo276 Otherinfo277 Otherinfo278 Otherinfo279 Otherinfo280 Otherinfo281 Otherinfo282 Otherinfo283 Otherinfo284 Otherinfo285 Otherinfo286 Otherinfo287 Otherinfo288 Otherinfo289 Otherinfo290 Otherinfo291 Otherinfo292 Otherinfo293 Otherinfo294 Otherinfo295 Otherinfo296 Otherinfo297 Otherinfo298 Otherinfo299 Otherinfo300 Otherinfo301 Otherinfo302 Otherinfo303 Otherinfo304 Otherinfo305 Otherinfo306 Otherinfo307 Otherinfo308 Otherinfo309 Otherinfo310 Otherinfo311 Otherinfo312 Otherinfo313 Otherinfo314 Otherinfo315 Otherinfo316 Otherinfo317 Otherinfo318 Otherinfo319 Otherinfo320 Otherinfo321
2 135788540 135788540 A G exonic LCT . synonymous SNV LCT:NM_002299:exon17:c.T5568C:p.A1856A Lactase deficiency, congenital, Autosomal recessive 2q21.3 0.6215 0.3853 0.5114 0.4403 0.7399 0.7288 0.5958 0.4622 rs2278544 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.4773 . . 2 135788540 . A G . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|1 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 1|1 0|0 0|1 0|1 0|0 0|0 0|0 0|1 0|0 1|0 0|0 1|0 0|0 0|1 0|1 1|0 1|1 1|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 1|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|1 1|0 0|0 0|0 1|0 1|0 0|1 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 1|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 1|1 1|0 0|0 1|0 0|0 0|0 0|1 0|1 1|0 1|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|1 1|0 1|1 0|1 0|1 0|1 1|1 0|0 1|1 0|0 1|1 1|0 0|0 0|1 1|0 1|0 0|0 1|1 1|1 0|1 1|0 0|1 0|1 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 1|0 0|1 1|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|1 1|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 1|1 0|1 0|0 0|1 0|1 0|0 0|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|1 0|0 0|1 0|0 1|1 0|0 0|0 0|0 0|0 1|1 1|0 0|0 1|0 0|0 0|1 0|0 0|0 0|0
2 135794124 135794124 C T intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs12998016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3900 . . 2 135794124 . C T . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 1|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|1 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 0|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|1 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
2 135795612 135795612 A T intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs1030766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.5890 . . 2 135795612 . A T . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 1|1 0|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 1|0 0|0 0|1 0|1 1|1 0|1 0|1 0|1 0|0 0|0 0|0 0|1 0|1 1|1 0|1 1|0 0|0 0|1 0|1 1|1 1|0 1|1 0|1 0|1 0|0 1|1 1|1 1|1 0|0 1|1 1|0 1|0 0|0 1|1 1|1 1|1 0|0 1|0 0|0 0|1 1|0 0|0 1|0 1|1 1|0 0|1 0|1 1|0 1|1 1|1 1|0 1|1 0|1 1|0 0|1 1|1 1|1 0|1 0|1 0|1 0|0 1|0 0|1 1|0 0|1 1|1 0|1 1|0 1|1 0|1 0|0 1|0 1|0 1|1 1|0 1|0 1|1 1|1 0|1 1|0 0|0 0|0 1|1 0|1 1|0 1|1 0|1 1|1 0|1 0|1 0|0 1|0 0|1 1|0 0|1 1|1 1|1 1|1 0|1 0|1 0|1 1|1 0|0 1|1 0|0 1|1 1|0 0|1 1|1 1|0 1|0 1|0 1|1 1|1 0|1 1|0 0|1 0|1 0|1 0|0 0|1 0|0 1|0 0|1 1|0 0|0 1|0 0|0 0|1 0|0 0|0 0|0 0|0 1|0 1|1 1|0 0|1 1|1 1|0 0|1 0|1 0|1 1|0 0|0 0|0 0|0 1|1 0|0 0|0 0|1 1|0 1|1 0|1 1|0 1|0 0|1 0|0 0|0 1|0 0|0 0|0 0|0 1|1 0|0 0|1 0|0 1|0 0|1 1|1 0|1 1|0 0|0 1|1 0|1 0|1 0|1 0|1 0|0 1|1 0|0 1|0 1|0 0|0 0|0 0|0 1|0 0|0 1|1 0|0 1|0 0|1 0|0 0|1 1|0 0|1 0|0 1|1 0|0 0|0 0|0 0|0 1|1 1|0 0|0 1|0 0|0 0|1 1|0 0|0 1|0
2 135796069 135796069 G A intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs1011361 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3900 . . 2 135796069 . G A . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 1|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|1 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 0|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|1 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
2 135797230 135797230 G C intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs6430589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3867 . . 2 135797230 . G C . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|0 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 1|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|1 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 0|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|0 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
2 135798089 135798089 T C exonic LCT . nonsynonymous SNV LCT:NM_002299:exon13:c.A4916G:p.N1639S Lactase deficiency, congenital, Autosomal recessive 2q21.3 0.6058 0.3969 0.4966 0.4790 0.7269 0.7003 0.5672 0.4520 rs2322659 0.134 T 0.013 B 0.031 B 0.152 N 1 P 0.28 N 1.54 T -0.1 N 0.088 -0.727 0.063 0.742 0.099 N -0.969 T 0.000 T 0.556 0 -8.89 0.018 -0.343 0.933 0.193 10.073 0.4790 . . 2 135798089 . T C . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|1 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 1|1 0|0 0|1 0|1 0|0 0|0 0|0 0|1 0|0 1|0 0|0 1|0 0|0 0|1 0|1 1|0 1|1 1|1 0|1 0|0 1|0 0|1 1|0 1|1 0|0 1|1 1|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|1 1|1 0|0 0|0 1|0 1|1 0|1 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 1|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 1|1 1|0 0|0 1|0 0|0 0|0 0|1 0|1 1|0 1|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|1 1|0 1|1 0|1 0|0 0|1 1|1 0|0 1|1 0|0 1|1 1|0 0|0 0|1 1|0 1|0 0|0 1|1 1|1 0|1 1|0 0|1 0|1 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 1|0 0|1 1|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|1 1|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 1|1 0|1 0|0 0|1 0|1 0|0 0|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|1 0|0 0|1 0|0 1|1 0|0 0|0 0|0 0|0 1|1 1|0 0|0 1|0 0|0 0|1 0|1 0|0 0|0
2 135816872 135816872 T - intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs34890037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.4013 . . 2 135816871 . AT A . PASS . GT 0|1 0|1 1|0 1|1 0|0 1|1 0|0 1|0 1|1 0|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|0 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|0 1|1 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|1 0|1 1|0 1|1 1|0 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|0 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|1 0|0 0|1 1|0 1|1 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 1|1 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 1|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 1|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 1|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|1 1|0 0|0 1|0 1|0 1|1 0|1 0|1 0|0 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|1 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 1|0 0|0 0|1 0|0 0|0 0|0 1|0 0|1 0|1 0|0 0|0 0|0 0|0 0|0
2 135829388 135829388 C A intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs10186843 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3883 . . 2 135829388 . C A . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 1|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 1|1 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|0 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
2 135830461 135830461 C A intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs73957037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3576 . . 2 135830461 . C A . PASS . GT 1|0 0|0 0|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|1 0|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|1 0|1 1|0 0|0 1|0 0|0 0|0 1|0 1|1 0|1 1|0 1|0 0|0 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 1|0 1|0 1|1 1|0 0|0 0|0 1|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 1|1 0|1 1|1 0|0 0|1 1|1 1|1 0|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 1|1 0|0 1|0 0|1 0|0 1|1 1|0 0|1 1|0 0|1 1|0 0|0 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|0 0|0 0|1 0|0 0|1 1|1 0|1 0|1 0|1 0|0 0|0 0|1 0|0 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 0|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 0|0 0|1 1|0 0|1 1|0 1|0 0|1 1|0 0|0 1|1 1|1 0|0 0|1 1|0 0|1 0|0 0|1 1|0 0|1 0|0 0|1 1|1 1|1 1|0 1|1 0|0 0|0 0|0 1|1 1|0 0|1 0|1 1|0 1|1 1|0 1|0 1|0 1|1 0|0 0|0 0|0 0|0 1|1 0|1 1|0 0|0 0|0 0|1 1|0 0|0 1|0 1|0 0|1 0|0 1|0 0|0 1|1 1|1 0|1 1|0 1|1 1|1 0|0 1|1 1|0 1|1 0|1 1|1 0|1 1|0 0|0 1|1 1|1 0|0 0|1 1|1 1|1 1|0 0|1 0|1 1|1 0|0 1|0 1|0 1|1 1|1 1|0
2 135830908 135830908 T A intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs10207652 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3883 . . 2 135830908 . T A . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 1|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|1 0|0 0|1 1|0 1|1 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 1|1 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|0 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
2 135831389 135831392 AGAG - intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs111825752 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3398 . . 2 135831388 . CAGAG C . PASS . GT 1|0 0|0 0|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|1 0|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|1 0|1 1|0 0|0 1|0 0|0 0|1 1|0 1|1 0|1 1|0 1|0 1|0 0|0 0|1 0|0 1|0 1|0 0|0 0|0 0|0 1|0 1|0 1|1 1|0 0|0 0|0 1|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 1|1 0|1 1|1 0|0 0|1 1|1 1|1 0|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 1|1 0|0 1|0 0|1 0|0 1|1 1|0 0|1 1|0 0|1 1|0 0|0 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|0 0|0 0|1 0|0 0|1 1|1 0|1 0|1 0|1 0|0 0|0 0|1 0|0 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 0|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 0|0 0|1 1|0 0|1 1|0 1|0 0|0 1|0 0|0 1|1 0|1 1|1 1|1 1|1 0|1 0|0 0|1 1|0 0|0 0|0 0|1 1|0 1|1 0|1 1|1 0|0 0|0 0|0 0|0 0|0 1|1 0|1 1|0 1|1 0|0 1|0 1|0 1|1 0|0 0|1 0|0 0|0 0|1 0|1 1|0 0|1 0|0 0|1 0|0 1|1 1|0 1|0 0|0 0|1 1|0 0|0 1|1 0|1 0|1 1|0 1|1 1|0 0|0 1|1 1|0 1|0 0|1 1|0 0|1 0|0 0|0 1|0 1|0 0|1 0|1 0|1 1|1 1|0 0|0 0|1 1|1 1|0 1|0 1|1 1|0 1|0 1|0
2 135831809 135831809 G A intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs11886852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3835 . . 2 135831809 . G A . PASS . GT 1|0 0|0 0|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|1 0|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|1 0|1 1|0 0|0 1|0 0|0 0|1 1|0 1|1 0|1 1|0 1|0 1|0 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 1|0 1|0 1|1 1|0 0|0 0|0 1|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 1|1 0|1 1|1 0|0 0|1 1|1 1|1 0|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 1|1 0|0 1|0 0|1 0|0 1|1 1|0 0|1 1|0 0|1 1|0 0|0 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|0 0|0 0|1 0|0 0|1 1|1 0|1 0|1 0|1 0|0 0|0 0|1 0|0 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 0|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 0|0 0|1 1|0 0|1 1|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 1|1 1|1 0|1 0|0 0|1 1|0 0|1 0|0 0|1 1|1 1|1 1|1 1|1 0|0 0|0 0|0 1|1 1|0 1|1 0|1 1|0 1|1 1|0 1|0 1|0 1|1 0|0 1|1 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|1 1|0 1|1 1|0 1|0 0|0 0|1 1|0 0|0 1|1 1|1 0|1 1|1 1|1 1|1 0|0 1|0 1|0 1|1 0|1 1|1 0|1 1|0 0|0 1|1 1|1 0|1 0|1 1|1 1|1 1|0 0|1 0|1 1|1 1|0 1|0 1|1 1|1 1|1 1|0
2 135832042 135832042 C G intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs12620033 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3851 . . 2 135832042 . C G . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 1|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|0 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
2 135832171 135832171 G A intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs61451678 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3851 . . 2 135832171 . G A . PASS . GT 1|0 0|0 0|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|1 0|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|1 0|1 1|0 0|0 1|0 0|0 0|1 1|0 1|1 0|1 1|0 1|0 1|0 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 1|0 1|0 1|1 1|0 0|0 0|0 1|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 1|1 0|1 1|1 0|0 0|1 1|1 1|1 0|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 1|1 0|0 1|0 0|1 0|0 1|1 1|0 0|1 1|0 0|1 1|0 0|0 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|0 0|0 0|1 0|0 0|1 1|1 0|1 0|1 0|1 0|0 0|0 0|1 0|0 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 0|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 0|0 0|1 1|0 0|1 1|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 1|1 1|1 0|1 0|0 0|1 1|0 0|1 0|0 0|1 1|1 1|1 1|1 1|1 0|0 0|0 0|0 1|1 1|0 1|1 0|1 1|0 1|1 1|0 1|0 1|0 1|1 0|0 1|1 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|1 1|0 1|1 1|0 1|0 0|1 0|1 1|0 0|0 1|1 1|1 0|1 1|1 1|1 1|1 0|0 1|0 1|0 1|1 0|1 1|1 0|1 1|0 0|0 1|1 1|1 0|1 0|1 1|1 1|1 1|0 0|1 0|1 1|1 1|0 1|0 1|1 1|1 1|1 1|0
2 135833176 135833176 C T exonic LCT . nonsynonymous SNV LCT:NM_002299:exon2:c.G655A:p.V219I Lactase deficiency, congenital, Autosomal recessive 2q21.3 0.2437 0.4610 0.2374 0.3891 0.1468 0.1938 0.2676 0.2745 rs3754689 1.0 T 0.009 B 0.026 B 0.289 N 0.999 P -0.47 N 1.79 T 0.01 N 0.037 -0.117 1.609 0.127 0.179 N -0.914 T 0.000 T 0.554 0 2.81 0.598 0.931 0.629 0.811 7.644 0.3867 . . 2 135833176 . C T . PASS . GT 1|0 0|0 0|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|1 0|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|1 0|1 1|0 0|0 1|0 0|0 0|1 1|0 1|1 0|1 1|0 1|0 1|0 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 1|0 1|0 1|1 1|0 0|0 0|0 1|1 0|0 1|0 0|0 1|1 1|0 0|0 0|0 1|1 0|1 1|1 0|0 0|1 1|1 1|1 0|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 1|1 0|0 1|0 0|1 0|0 1|1 1|0 0|1 1|0 0|1 1|0 0|0 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|0 0|0 0|1 0|0 0|1 1|1 0|1 0|1 0|1 0|0 0|0 0|1 0|0 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 0|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 0|0 0|1 1|0 0|1 1|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 1|1 1|1 0|1 0|0 0|1 1|0 0|1 0|0 0|1 1|1 1|1 1|1 1|1 0|0 0|0 0|0 1|1 1|0 1|1 0|1 1|0 1|1 1|0 1|0 1|0 1|1 0|0 1|1 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|1 1|0 1|1 1|0 1|0 0|1 0|1 1|0 0|0 1|1 1|1 0|1 1|1 1|1 1|1 0|0 1|0 1|0 1|1 0|1 1|1 0|1 1|0 0|0 1|1 1|1 0|1 0|1 1|1 1|1 1|0 0|1 0|1 1|1 1|0 1|0 1|1 1|1 1|1 1|0
2 135834289 135834289 G A intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs62159034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3851 . . 2 135834289 . G A . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 1|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|0 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
2 135836108 135836108 T C intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs11895319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3803 . . 2 135836108 . T C . PASS . GT 1|0 0|0 0|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|1 0|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 1|0 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|1 0|1 1|0 0|0 1|0 0|0 0|1 1|0 1|1 0|1 1|0 1|0 1|0 0|0 1|1 0|0 1|1 1|0 0|0 0|0 0|0 1|0 1|0 1|1 1|0 0|0 0|0 1|1 0|0 1|0 0|0 1|1 0|0 0|0 0|0 1|1 0|1 1|1 0|0 0|1 1|1 1|1 0|1 0|1 1|0 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 1|1 0|0 1|0 0|1 0|0 1|1 1|0 0|1 1|0 0|1 1|0 0|0 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|0 0|0 0|1 0|0 0|1 1|1 0|1 0|1 0|1 0|0 0|0 0|1 0|0 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 0|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|0 0|0 0|1 1|0 0|1 1|0 1|0 0|1 1|0 0|0 1|1 0|1 1|1 1|1 1|1 0|1 0|0 0|1 1|0 0|1 0|0 0|1 1|1 1|1 1|1 1|1 0|0 0|0 0|0 1|1 1|0 1|1 0|1 1|0 1|1 1|0 1|0 1|0 1|1 0|0 1|1 0|0 0|0 1|1 0|1 1|0 0|1 0|0 0|1 1|0 1|1 1|0 1|0 0|1 0|1 1|0 0|0 1|1 1|1 0|1 1|1 1|1 1|1 0|0 1|0 1|0 1|1 0|1 1|1 0|1 1|0 0|0 1|1 1|1 0|1 0|1 1|1 1|1 1|0 0|1 0|1 1|1 1|0 0|0 1|1 1|1 1|1 1|0
2 135836190 135836190 G T intronic LCT . . . Lactase deficiency, congenital, Autosomal recessive 2q21.3 . . . . . . . . rs6730196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.5922 . . 2 135836190 . G T . PASS . GT 1|0 1|0 0|1 0|0 1|0 0|0 1|1 0|1 0|0 0|0 0|0 0|0 0|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 1|0 0|0 0|1 0|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|1 0|0 0|0 1|0 0|0 0|1 0|0 0|0 0|0 1|0 1|0 0|0 1|1 0|1 0|0 1|0 0|0 0|0 1|0 1|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 0|0 0|0 1|0 0|1 0|0 0|0 0|0 0|0 1|0 1|1 1|1 0|1 1|0 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 0|1 0|0 1|0 1|0 1|1 1|1 1|0 0|1 0|0 1|1 0|0 1|1 0|0 1|1 1|0 0|0 0|0 1|1 0|1 1|1 1|1 0|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|0 0|0 1|1 0|1 1|0 1|1 1|1 0|0 1|0 1|1 1|0 1|1 1|1 1|1 1|0 0|1 1|0 1|0 1|0 1|1 1|1 1|1 1|1 1|1 0|1 0|0 0|1 0|1 1|0 0|1 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|0 1|1 1|1 1|0 1|1 1|1 1|1 0|1 1|1 0|1 1|1 0|0 1|0 1|0 1|1 0|0 1|1 0|0 1|1 0|0 1|1 1|1 1|0 1|1 0|1 1|1 1|1 0|0 1|0 1|1 1|0 1|1 1|1 1|1 1|1 0|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|0 1|1 1|1 1|1 0|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1
2 135836588 135836588 G A exonic LCT . synonymous SNV LCT:NM_002299:exon1:c.C582T:p.T194T Lactase deficiency, congenital, Autosomal recessive 2q21.3 0.5487 0.2204 0.3946 0.3654 0.7022 0.6696 0.5253 0.4110 rs2236783 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.3851 . . 2 135836588 . G A . PASS . GT 0|1 0|1 1|0 1|1 0|1 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 1|1 0|1 1|1 1|1 0|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 0|1 0|1 1|1 0|0 1|0 1|1 0|1 1|1 1|1 0|1 0|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 1|1 0|1 0|1 0|0 0|0 0|1 1|0 1|1 0|0 1|1 0|0 1|1 0|0 0|1 1|1 1|1 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 1|0 0|0 0|1 0|0 0|1 1|1 0|0 1|0 0|1 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|1 1|0 0|1 0|1 0|1 0|0 0|0 0|0 0|0 0|0 1|0 1|1 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 0|1 0|1 1|0 1|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 1|0 0|0 1|0 0|0 1|1 0|1 0|1 0|0 1|1 0|0 1|1 0|0 1|1 0|0 0|0 0|1 0|0 1|0 0|0 0|0 1|1 0|1 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0

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